diff --git a/src/castep_castep_reader.cpp b/src/castep_castep_reader.cpp
index f6c38a508d7b4ab72f1f85f7685f08134427719d..b04545e23bf2247f7df710997d9d6e30248d109e 100644
--- a/src/castep_castep_reader.cpp
+++ b/src/castep_castep_reader.cpp
@@ -28,281 +28,698 @@ void CastepCastepReader::read_data(const std::string& filename) {
}
void CastepCastepReader::parse_data() {
- std::istringstream stream(raw_data_);
- std::string line;
+ // Enumerates possible parse states for line-by-line scanning
+ enum class CalcState {
+ Idle, // No recognized computation
+ GeometryOptimization,
+ MolecularDynamics,
+ SinglePoint // SCF or single-point run
+ };
- size_t natoms;;
- bool stress_tensor_bool = false;
- bool constant_volume = false;
- bool complete_structure = false;
- bool md_run = false;
- bool go_run = false;
- bool restart = false;
- int scf_idx = 0;
+ // Current parser state and relevant flags
+ CalcState current_state = CalcState::Idle;
+ bool stress_tensor_found = false;
+ bool data_block_complete = false; // Indicates a completed set of structure data
+ bool is_stress = false; // SCF run with stress tensor
- Structure s;
- std::string label;
- size_t counter=0;
+ // Local counters and accumulators
+ size_t natoms = 0; // Number of atoms from the input
+ int scf_counter = 0; // Index for SCF runs (tracking distinct single-point steps)
+ size_t line_counter = 0; // Tracks line number for warnings
+ bool debug = false; // Local debug toggle
- bool debug = false;
+ // Temporary container to hold ongoing parse results
+ Structure s;
+ std::vector<Atom> atoms;
- while (std::getline(stream, line)) {
-
- if (line.find("type of calculation") != std::string::npos) {
- stress_tensor_bool=false;
- constant_volume=false;
- md_run = false;
- go_run = false;
- restart=false;
- if (line.find(": geometry optimization") != std::string::npos) {
- if (debug) std::cout << "GO run" << std::endl;
- go_run = true;
- }
- if (line.find(": molecular dynamics") != std::string::npos) {
- md_run = true;
- }
+ // Internal helper to finalize a structure's data:
+ // This updates derived data (like stress if absent) and adds to the structure DB.
+ auto finalize_structure = [&]() {
+ // If stress tensor was not parsed, set it to zero
+ if (!stress_tensor_found) {
+ s.stress.set_zero();
+ } else {
+ s.stress *= p_conv; // Convert from GPa to eV/ų
}
- else if (line.find("Restarting MD") != std::string::npos) {
- restart=true;
+ // We have to compute absolute positions here from temporary fractional positions
+ // In case of volume-only relaxation fractional positions are reported only once
+ s.atoms.resize(atoms.size());
+ for (size_t i = 0; i < atoms.size(); ++i) {
+ s.atoms[i].position = s.cell * atoms[i].position;
+ s.atoms[i].force = atoms[i].force;
+ s.atoms[i].symbol = atoms[i].symbol;
}
- else if (line.find("Unit Cell") != std::string::npos) {
- if (debug) std::cout << "Unit Cell" << std::endl;
- if (!std::getline(stream, line) || !std::getline(stream, line)) {
- std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
- std::cerr << "Warning: Unexpected end of data when reading atom information" << std::endl;
- }
- counter++;
- counter++;
+ stdb.add(s);
+ };
+
+ auto reset_flags = [&](CalcState new_state) {
+ current_state = new_state;
+ stress_tensor_found = false;
+ data_block_complete = false;
+ if (debug) std::cout << "Resetting flags for new calculation type" << std::endl;
+ };
+
+ // Use a string stream to iterate over lines in raw_data_
+ std::istringstream stream(raw_data_);
+ std::string line;
+ while (std::getline(stream, line)) {
+ ++line_counter;
- s = Structure();
+ // Detect or store the "Unit Cell"
+ if (line.find("Unit Cell") != std::string::npos) {
+ // A new cell is encountered. Prepare to read the next three lines of vectors.
+ // Finalize any incomplete data set if logic demands it, but not strictly necessary here
+ if (debug) std::cout << "Reading 3 lines of Unit Cell" << std::endl;
+
+ // Skip the next two lines, often blank or headers
+ if (!std::getline(stream, line)) break;
+ ++line_counter;
+ if (!std::getline(stream, line)) break;
+ ++line_counter;
+
+ // Read the 3 lattice vectors
for (int i = 0; i < 3; ++i) {
if (!std::getline(stream, line)) {
- std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
- std::cerr << "Warning: Unexpected end of data when reading lattice vectors at row " << i << std::endl;
+ std::cerr << "Warning: Unexpected end of file while reading lattice vectors at row "
+ << i << " (line: " << line_counter << ")." << std::endl;
break;
}
- counter++;
+ ++line_counter;
std::istringstream iss(line);
- if (!(iss >> s.cell(0,i) >> s.cell(1,i) >> s.cell(2,i))) {
- std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
- std::cerr << "Warning: Unexpected end of data when reading lattice vectors at row " << i << std::endl;
+ if (!(iss >> s.cell(0, i) >> s.cell(1, i) >> s.cell(2, i))) {
+ std::cerr << "Warning: Failed to parse lattice vector at row "
+ << i << " (line: " << line_counter << ")." << std::endl;
break;
}
}
-
- if (constant_volume) label.clear();
- constant_volume = false;
- if (debug) std::cout << s.cell << std::endl;
+ continue;
}
- else if (line.find("Total number of ions in cell") != std::string::npos) {
- // this line indicates new type of computation, so we reset flags here
+ // Detect total number of ions
+ if (line.find("Total number of ions in cell") != std::string::npos) {
+ // Parse the integer natoms from this line
std::istringstream iss(line);
- std::string temp;
- int count = 0;
-
- // Process the line to reach the 8th element
- while (iss >> temp) {
- if (++count == 7 && !(iss >> natoms)) {
- std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
- std::cerr << "Error: Failed to read number of atoms from line: " << line << std::endl;
+ std::string tmp;
+ int word_count = 0;
+ while (iss >> tmp) {
+ ++word_count;
+ if (word_count == 7) {
+ if (!(iss >> natoms)) {
+ std::cerr << "Warning: Could not parse number of atoms in line: " << line_counter << std::endl;
+ }
+ break;
}
}
+ if (debug) std::cout << "Total number of ions in cell: " << natoms << std::endl;
+ continue;
+ }
- // Check if the line was too short
- if (count < 7) {
- std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
- std::cerr << "Error: Line is too short to extract total number of ions in a cell. Line: " << line << std::endl;
- }
- if (debug) std::cout << "Number of atoms: " << natoms << std::endl;
+ // Detect starting MD iteration
+ if (line.find("Starting MD iteration") != std::string::npos) {
+ reset_flags(CalcState::MolecularDynamics);
+ std::istringstream iss(line);
+ std::string ignore, step;
+ iss >> ignore >> ignore >> ignore >> step;
+
+ // Remove last step from label
+ while (s.label.back() != ' ')
+ s.label.pop_back();
+
+ s.label += step;
+
+ if (debug) std::cout << "Starting MD iteration " << step << std::endl;
+ continue;
}
- else if (line.find("so fixing cell parameters") != std::string::npos) {
- if (debug) std::cout << "so fixing cell parameters" << std::endl;
- constant_volume=true;
- label = "CASTEP MD, const. volume: true, step: 0";
+ // Detect starting SP calculation (zeroth step)
+ if (line.find("single point energy") != std::string::npos) {
+ reset_flags(CalcState::SinglePoint);
+ if (!std::getline(stream, line)) break;
+ ++line_counter;
+ std::istringstream iss(line);
+ std::string ignore, stress;
+ iss >> ignore >> ignore >> ignore >> stress;
+ s.label = "File: " + filename + " | CASTEP single point calculation, stress: " + stress;
+ if (stress == "on") {
+ is_stress = true;
+ }
+ else {
+ is_stress = false;
+ }
+ if (debug) std::cout << "single point energy" << std::endl;
}
- else if (line.find("Starting MD iteration") != std::string::npos) {
- if (debug) std::cout << "Starting MD iteration" << std::endl;
+ // Detect starting GO iteration (zeroth step)
+ if (line.find("Geometry Optimization Parameters") != std::string::npos) {
+ reset_flags(CalcState::GeometryOptimization);
+ std::string ignore, algo;
+
+ if (!std::getline(stream, line)) break;
+ ++line_counter;
+ if (!std::getline(stream, line)) break;
+ ++line_counter;
std::istringstream iss(line);
- std::string step;
- iss >> step >> step >> step >> step;
- std::ostringstream oss;
- oss << std::boolalpha << constant_volume;
- label = "CASTEP MD, const. volume: " + oss.str() + ", step: " + step;
+ iss >> ignore >> ignore >> ignore >> algo;
+ s.label = "File: " + filename + " | CASTEP GO, "+algo+ ", step: ";
+ if (debug) std::cout << "Geometry Optimization Parameters" << std::endl;
}
+ // Detect starting MD simulation (zeroth step)
+ if (line.find("Molecular Dynamics Parameters") != std::string::npos) {
+ reset_flags(CalcState::MolecularDynamics);
- else if (constant_volume && line.find("Cell Contents") != std::string::npos) {
- if (debug) std::cout << "Cell Contents" << std::endl;
- if (restart) {
- if (debug) std::cout << "Cell Contents restart" << std::endl;
- s.atoms.clear();
- } else {
- if (debug) std::cout << "Cell Contents no restart" << std::endl;
- if (debug) std::cout << line << std::endl;
- s = Structure();
- s.cell = stdb.structures.back().cell; // copy last cell as it is not repeated in castep for const. volume
- }
+ if (!std::getline(stream, line)) break;
+ ++line_counter;
+ if (!std::getline(stream, line)) break;
+ ++line_counter;
+ std::istringstream iss(line);
+ std::string ignore, ensemble;
+ iss >> ignore >> ignore >> ensemble;
+ s.label = "File: " + filename + " | CASTEP MD, "+ensemble+" step: " + "0";
+ if (debug) std::cout << "Molecular Dynamics Parameters" << std::endl;
+ continue;
+ }
+
+ // Detect starting GO iteration
+ if (line.find("Starting BFGS iteration") != std::string::npos ||
+ line.find("Starting LBFGS iteration") != std::string::npos ||
+ line.find("Starting Delocalized iteration") != std::string::npos ||
+ line.find("Starting DampedMD iteration") != std::string::npos ||
+ line.find("Starting TPSD iteration") != std::string::npos) {
+ reset_flags(CalcState::GeometryOptimization);
+ // This line often carries the iteration number
+ std::istringstream iss(line);
+ std::string ignore, algo, step_str;
+ // The typical format: "Starting MD iteration N ..."
+ // Attempt to parse out the iteration number as step_str
+ iss >> ignore >> algo >> ignore >> step_str;
+ // Store it in a label for clarity
+ s.label = "File: " + filename + " | CASTEP GO, "+algo+" step: ";
+ if (debug) std::cout << "Starting" +algo+ " iteration " << step_str << std::endl;
+ continue;
}
- else if (line.find("Fractional coordinates of atoms") != std::string::npos) {
+ // if (line.find("finished MD iteration") != std::string::npos) {
+ // reset_flags(CalcState::Idle);
+ // }
+
+ // Detect fractional coordinates block
+ if (line.find("Fractional coordinates of atoms") != std::string::npos) {
if (debug) std::cout << "Fractional coordinates of atoms" << std::endl;
- // Ideally st.natoms() should be zero by now. However for constant volum GO this is not the case.
- // Therfore we need to clear the atoms vector but we keep the st.cell as it is.
- s.atoms.clear();
- if (!std::getline(stream, line) || !std::getline(stream, line)) {
- std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
- std::cerr << "Warning: Unexpected end of data when reading atom information" << std::endl;
- }
- counter++;
- counter++;
+ // Typically followed by two header/blank lines
+ if (!std::getline(stream, line)) break;
+ ++line_counter;
+ if (!std::getline(stream, line)) break;
+ ++line_counter;
+ // If constant volume, the code does not always reprint the cell.
+ // The logic here re-uses the last known cell if needed.
+ atoms.clear(); // Clear old atoms or partial data
+
+ atoms.reserve(natoms);
for (size_t i = 0; i < natoms; ++i) {
if (!std::getline(stream, line)) {
- std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
- std::cerr << "Warning: Unexpected end of data when reading atomic coordinates at row " << i << std::endl;
+ std::cerr << "Warning: Truncated file reading fractional coords at row " << i
+ << " (line: " << line_counter << ")." << std::endl;
break;
}
- counter++;
+ ++line_counter;
+
+ // Format is typically: " X ??? ??? frac_x frac_y frac_z "
std::istringstream iss(line);
- std::string type, tmp;
- double px,py,pz;
- if (!(iss >> tmp >> type >> tmp >> px >> py >> pz)) {
- std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
- std::cerr << "Warning: Unexpected end of data when reading atomic coordiantes at row " << i << std::endl;
+ std::string discard, species;
+ double px, py, pz;
+ if (!(iss >> discard >> species >> discard >> px >> py >> pz)) {
+ std::cerr << "Warning: Unexpected parse error reading fractional coords (line: "
+ << line_counter << ")." << std::endl;
break;
}
- s.add_atom(Atom(Element(type),px,py,pz,0,0,0));
- s.atoms[i].position = s.cell * s.atoms[i].position; // convert to abs
+ // Create Atom, convert fractional to absolute using s.cell
+ Atom a(Element(species), px, py, pz, 0.0, 0.0, 0.0);
+ atoms.push_back(a); // keep it fractional for now
}
- if (debug) std::cout << "natoms: " << s.natoms() << std::endl;
+ continue;
}
- else if (line.find("Cartesian components (eV/A)") != std::string::npos) {
- if (debug) std::cout << "Cartesian components (eV/A)" << std::endl;
- if (s.natoms()!=natoms) continue;
- if (!std::getline(stream, line) || !std::getline(stream, line) || !std::getline(stream, line)) {
- std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
- std::cerr << "Warning: Unexpected end of data when reading atom forces" << std::endl;
+ // The old cell is reverted and printed before final enthalpy from the current iteration
+ // We simply skip over this block of text
+ if (line.find("reverting to earlier configuration") != std::string::npos) {
+ if (debug) std::cout << "reverting to earlier configuration" << std::endl;
+ for (int i = 0; i < 30; ++i) {
+ if (!std::getline(stream, line)) {
+ std::cerr << "Warning: Failed skiping over revered configuration " << line_counter << ")." << std::endl;
+ break;
+ }
+ ++line_counter;
+ }
+ }
+
+ // Detect forces block
+ if (line.find("Cartesian components (eV/A)") != std::string::npos) {
+ if (debug) std::cout << "Reading forces..." << std::endl;
+ // Usually there are three lines of header/blank text before actual force lines
+ for (int i = 0; i < 3; ++i) {
+ if (!std::getline(stream, line)) {
+ std::cerr << "Warning: Incomplete forces header block (line: " << line_counter << ")." << std::endl;
+ break;
+ }
+ ++line_counter;
}
- counter++;
- counter++;
- counter++;
+ // Read force for each atom
for (size_t i = 0; i < natoms; ++i) {
if (!std::getline(stream, line)) {
- std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
- std::cerr << "Warning: Unexpected end of data when reading atom forces: " << line << std::endl;
+ std::cerr << "Warning: Truncated file reading forces at row " << i
+ << " (line: " << line_counter << ")." << std::endl;
break;
}
- counter++;
+ ++line_counter;
+
std::istringstream iss(line);
std::string tmp;
- double fx,fy,fz;
+ double fx, fy, fz;
+ // Format typically: " ??? ??? ??? fx fy fz "
if (!(iss >> tmp >> tmp >> tmp >> fx >> fy >> fz)) {
- std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
- std::cerr << "Warning: Unexpected end of data when reading atom forces: " << line << std::endl;
- } else {
- s.atoms[i].force = Vec3d(fx,fy,fz);
+ std::cerr << "Warning: Could not parse atomic forces (line: "
+ << line_counter << ")." << std::endl;
+ break;
+ }
+ // Assign force to the matching atom
+ if (i < atoms.size()) {
+ atoms[i].force = Vec3d(fx, fy, fz);
}
}
+ continue;
}
- else if (line.find("Cartesian components (GPa)") != std::string::npos) {
- if (debug) std::cout << "Cartesian components (GPa)" << std::endl;
- if (!std::getline(stream, line) || !std::getline(stream, line) || !std::getline(stream, line)) {
- std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
- std::cerr << "Warning: Unexpected end of data when reading stress tensor" << std::endl;
+ // Detect stress block
+ if (line.find("Cartesian components (GPa)") != std::string::npos) {
+ if (debug) std::cout << "Reading stress..." << std::endl;
+ // Usually there are three lines of header/blank text
+ for (int i = 0; i < 3; ++i) {
+ if (!std::getline(stream, line)) {
+ std::cerr << "Warning: Incomplete stress header block (line: " << line_counter << ")." << std::endl;
+ break;
+ }
+ ++line_counter;
}
- counter++;
- counter++;
- counter++;
- for (size_t i = 0; i < 3; ++i) {
+ // A 3x3 matrix is expected
+ for (int row = 0; row < 3; ++row) {
if (!std::getline(stream, line)) {
- std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
- std::cerr << "Warning: Unexpected end of data when reading stress tensor: " << line << std::endl;
+ std::cerr << "Warning: Truncated file reading stress row " << row
+ << " (line: " << line_counter << ")." << std::endl;
break;
}
- counter++;
+ ++line_counter;
std::istringstream iss(line);
- std::string tmp;
- if (!(iss >> tmp >> tmp >> s.stress(i,0) >> s.stress(i,1) >> s.stress(i,2))) {
- std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
- std::cerr << "Warning: Unexpected end of data when reading atom forces: " << line << std::endl;
- }
+ std::string ignore;
+ double v1, v2, v3;
+ // Format: " ??? ??? val1 val2 val3 "
+ if (!(iss >> ignore >> ignore >> v1 >> v2 >> v3)) {
+ std::cerr << "Warning: Could not parse stress row (line: "
+ << line_counter << ")." << std::endl;
+ break;
+ }
+ s.stress(row, 0) = v1;
+ s.stress(row, 1) = v2;
+ s.stress(row, 2) = v3;
+ }
+ stress_tensor_found = true;
+ if (current_state == CalcState::SinglePoint) {
+ s.label += " SCF run: " + std::to_string(scf_counter++);
+ if (is_stress) data_block_complete = true;
}
- stress_tensor_bool = true;
+ continue;
}
- // Potential Energy // MD
- // Total energy corrected for finite basis set = -2690.182502 eV // GO, first step only
- // enthalpy= indicates end of iteration for GO
- else if (line.find("Final free energy (E-TS)") != std::string::npos) {
+ // Detect final free energy for single-point or last iteration in GO
+ if (line.find("Final free energy (E-TS)") != std::string::npos &&
+ (current_state == CalcState::GeometryOptimization || current_state == CalcState::SinglePoint)) {
if (debug) std::cout << "Final free energy (E-TS)" << std::endl;
+ // Single point or final iteration of a geometry optimization
std::istringstream iss(line);
- std::string tmp;
- if (!(iss >> tmp >> tmp >> tmp >> tmp >> tmp >> s.energy)) {
- std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
- std::cerr << "Warning: Unexpected end of data when reading total energy" << std::endl;
+ std::string ignore;
+ double energy;
+ // Typical: "Final free energy (E-TS) = <val> eV"
+ // Rolling through tokens to read last numeric:
+ if (!(iss >> ignore >> ignore >> ignore >> ignore >> ignore >> energy)) {
+ std::cerr << "Warning: Could not parse final free energy (line: "
+ << line_counter << ")." << std::endl;
+ } else {
+ s.energy = energy;
}
- // scf only loop
- if (!md_run && !go_run) {
- s.label = "SCF run: " + std::to_string(scf_idx++);
- complete_structure = true;
+
+ // Single-point detection: if current_state is Idle or SinglePoint, treat it as an SCF run
+ // but it might also appear mid-GO. The code below sets a label if no other structure data is present.
+ if (current_state == CalcState::SinglePoint && !is_stress) {
+ s.label += " SCF run: " + std::to_string(scf_counter++);
+ data_block_complete = true;
}
+ // Mark that data is complete for this structure
+ continue;
}
- else if (line.find("enthalpy=") != std::string::npos) {
+ // Detect the line with "enthalpy=" used in geometry optimization
+ if (line.find("enthalpy=") != std::string::npos && current_state == CalcState::GeometryOptimization) {
if (debug) std::cout << "enthalpy=" << std::endl;
- // GO: the last extracted free energy is correct one!
+ // This typically indicates a converged or final iteration of geometry optimization
std::istringstream iss(line);
- std::string step;
- iss >> step >> step >> step >> step; // safe as found enthalpy=
- std::ostringstream oss;
- oss << std::boolalpha << constant_volume;
- s.label = "CASTEP GO, const. volume: " + oss.str() + ", step: " + step;
- complete_structure = true;
+ std::string ignore, step;
+ if (!(iss >> ignore >> ignore >> ignore>> step >> ignore >> ignore >> s.energy)) {
+ std::cerr << "Warning: Could not parse final free energy (line: "
+ << line_counter << ")." << std::endl;
+ }
+ s.label += step;
+ data_block_complete = true;
+ continue;
}
- else if (line.find("Potential Energy:") != std::string::npos) {
+ // Detect potential energy line used in MD
+ if (line.find("Potential Energy:") != std::string::npos && current_state == CalcState::MolecularDynamics) {
if (debug) std::cout << "Potential Energy:" << std::endl;
+ // Format: "Potential Energy: <value>"
std::istringstream iss(line);
- std::string tmp;
- if (!(iss >> tmp >> tmp >> tmp >> s.energy)) {
- std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
- std::cerr << "Warning: Unexpected end of data when reading total energy" << std::endl;
+ std::string ignore;
+ double energy;
+ if (!(iss >> ignore >> ignore >> ignore >> energy)) {
+ std::cerr << "Warning: Could not parse potential energy in MD (line: "
+ << line_counter << ")." << std::endl;
+ } else {
+ s.energy = energy;
}
+ continue;
}
- else if (line.find("Temperature:") != std::string::npos) {
+
+ // Detect temperature line in MD, which often appears last in an MD step
+ if (line.find("Temperature:") != std::string::npos && current_state == CalcState::MolecularDynamics) {
if (debug) std::cout << "Temperature:" << std::endl;
- // MD: end of iteration
+ // This usually concludes an MD iteration
std::istringstream iss(line);
- std::string tmp;
- if (!(iss >> tmp >> tmp >> s.T)) {
- std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
- std::cerr << "Warning: Unexpected end of data when reading temperature" << std::endl;
+ std::string ignore;
+ double temperature;
+ // Format: "Temperature: <value>"
+ if (!(iss >> ignore >> ignore >> temperature)) {
+ std::cerr << "Warning: Could not parse temperature in MD (line: "
+ << line_counter << ")." << std::endl;
+ } else {
+ s.T = temperature;
}
-
- if (!label.size())label = "CASTEP MD, const. volume: false, step: 0"; // the last option
- s.label = label;
- complete_structure = true;
+ // If a label has not been set, create a fallback
+ // if (s.label.empty()) {
+ // s.label = "CASTEP MD step (no step # found)";
+ // }
+ data_block_complete = true;
+ continue;
}
- if (complete_structure) {
- if (!stress_tensor_bool) {
- s.stress.set_zero();
- }
- else {
- s.stress *= p_conv; // GPa -> eV/A^3
- }
- stdb.add(s);
- complete_structure = false;
+
+ // If a completed data set is detected, finalize
+ if (data_block_complete) {
+ finalize_structure();
+ reset_flags(CalcState::Idle);
}
- counter++;
- }
+ } // end while getline
+ // At file end, if a data block was incomplete but has partial data,
+ // it can either be discarded or stored as partial.
+ // For safety, only store if data_block_complete was triggered.
+ // No action is taken here unless a user-specific policy is desired.
}
+// void CastepCastepReader::parse_data() {
+// std::istringstream stream(raw_data_);
+// std::string line;
+//
+// size_t natoms;;
+// bool stress_tensor_bool = false;
+// bool constant_volume = false;
+// bool complete_structure = false;
+// bool md_run = false;
+// bool go_run = false;
+// bool restart = false;
+// int scf_idx = 0;
+//
+// Structure s;
+// std::string label;
+// size_t counter=0;
+//
+// bool debug = false;
+//
+// while (std::getline(stream, line)) {
+//
+// if (line.find("type of calculation") != std::string::npos) {
+// stress_tensor_bool=false;
+// constant_volume=false;
+// md_run = false;
+// go_run = false;
+// restart=false;
+// if (line.find(": geometry optimization") != std::string::npos) {
+// if (debug) std::cout << "GO run" << std::endl;
+// go_run = true;
+// }
+// if (line.find(": molecular dynamics") != std::string::npos) {
+// md_run = true;
+// }
+// }
+// else if (line.find("Restarting MD") != std::string::npos) {
+// restart=true;
+// }
+// else if (line.find("Unit Cell") != std::string::npos) {
+// if (debug) std::cout << "Unit Cell" << std::endl;
+// if (!std::getline(stream, line) || !std::getline(stream, line)) {
+// std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
+// std::cerr << "Warning: Unexpected end of data when reading atom information" << std::endl;
+// }
+// counter++;
+// counter++;
+//
+// s = Structure();
+// for (int i = 0; i < 3; ++i) {
+// if (!std::getline(stream, line)) {
+// std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
+// std::cerr << "Warning: Unexpected end of data when reading lattice vectors at row " << i << std::endl;
+// break;
+// }
+// counter++;
+// std::istringstream iss(line);
+// if (!(iss >> s.cell(0,i) >> s.cell(1,i) >> s.cell(2,i))) {
+// std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
+// std::cerr << "Warning: Unexpected end of data when reading lattice vectors at row " << i << std::endl;
+// break;
+// }
+// }
+//
+// if (constant_volume) label.clear();
+// constant_volume = false;
+// if (debug) std::cout << s.cell << std::endl;
+// }
+//
+// else if (line.find("Total number of ions in cell") != std::string::npos) {
+// // this line indicates new type of computation, so we reset flags here
+// std::istringstream iss(line);
+// std::string temp;
+// int count = 0;
+//
+// // Process the line to reach the 8th element
+// while (iss >> temp) {
+// if (++count == 7 && !(iss >> natoms)) {
+// std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
+// std::cerr << "Error: Failed to read number of atoms from line: " << line << std::endl;
+// }
+// }
+//
+// // Check if the line was too short
+// if (count < 7) {
+// std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
+// std::cerr << "Error: Line is too short to extract total number of ions in a cell. Line: " << line << std::endl;
+// }
+// if (debug) std::cout << "Number of atoms: " << natoms << std::endl;
+// }
+//
+// else if (line.find("so fixing cell parameters") != std::string::npos) {
+// if (debug) std::cout << "so fixing cell parameters" << std::endl;
+// constant_volume=true;
+// label = "CASTEP MD, const. volume: true, step: 0";
+// }
+//
+// else if (line.find("Starting MD iteration") != std::string::npos) {
+// if (debug) std::cout << "Starting MD iteration" << std::endl;
+// std::istringstream iss(line);
+// std::string step;
+// iss >> step >> step >> step >> step;
+// std::ostringstream oss;
+// oss << std::boolalpha << constant_volume;
+// label = "CASTEP MD, const. volume: " + oss.str() + ", step: " + step;
+// }
+//
+//
+// else if (constant_volume && line.find("Cell Contents") != std::string::npos) {
+// if (debug) std::cout << "Cell Contents" << std::endl;
+// if (restart) {
+// if (debug) std::cout << "Cell Contents restart" << std::endl;
+// s.atoms.clear();
+// } else {
+// if (debug) std::cout << "Cell Contents no restart" << std::endl;
+// if (debug) std::cout << line << std::endl;
+// s = Structure();
+// s.cell = stdb.structures.back().cell; // copy last cell as it is not repeated in castep for const. volume
+// }
+// }
+//
+// else if (line.find("Fractional coordinates of atoms") != std::string::npos) {
+// if (debug) std::cout << "Fractional coordinates of atoms" << std::endl;
+// // Ideally st.natoms() should be zero by now. However for constant volum GO this is not the case.
+// // Therfore we need to clear the atoms vector but we keep the st.cell as it is.
+// s.atoms.clear();
+// if (!std::getline(stream, line) || !std::getline(stream, line)) {
+// std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
+// std::cerr << "Warning: Unexpected end of data when reading atom information" << std::endl;
+// }
+// counter++;
+// counter++;
+//
+// for (size_t i = 0; i < natoms; ++i) {
+// if (!std::getline(stream, line)) {
+// std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
+// std::cerr << "Warning: Unexpected end of data when reading atomic coordinates at row " << i << std::endl;
+// break;
+// }
+// counter++;
+// std::istringstream iss(line);
+// std::string type, tmp;
+// double px,py,pz;
+// if (!(iss >> tmp >> type >> tmp >> px >> py >> pz)) {
+// std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
+// std::cerr << "Warning: Unexpected end of data when reading atomic coordiantes at row " << i << std::endl;
+// break;
+// }
+// s.add_atom(Atom(Element(type),px,py,pz,0,0,0));
+// s.atoms[i].position = s.cell * s.atoms[i].position; // convert to abs
+// }
+// if (debug) std::cout << "natoms: " << s.natoms() << std::endl;
+// }
+//
+// else if (line.find("Cartesian components (eV/A)") != std::string::npos) {
+// if (debug) std::cout << "Cartesian components (eV/A)" << std::endl;
+// if (s.natoms()!=natoms) continue;
+// if (!std::getline(stream, line) || !std::getline(stream, line) || !std::getline(stream, line)) {
+// std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
+// std::cerr << "Warning: Unexpected end of data when reading atom forces" << std::endl;
+// }
+// counter++;
+// counter++;
+// counter++;
+// for (size_t i = 0; i < natoms; ++i) {
+// if (!std::getline(stream, line)) {
+// std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
+// std::cerr << "Warning: Unexpected end of data when reading atom forces: " << line << std::endl;
+// break;
+// }
+// counter++;
+// std::istringstream iss(line);
+// std::string tmp;
+// double fx,fy,fz;
+// if (!(iss >> tmp >> tmp >> tmp >> fx >> fy >> fz)) {
+// std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
+// std::cerr << "Warning: Unexpected end of data when reading atom forces: " << line << std::endl;
+// } else {
+// s.atoms[i].force = Vec3d(fx,fy,fz);
+// }
+// }
+// }
+//
+// else if (line.find("Cartesian components (GPa)") != std::string::npos) {
+// if (debug) std::cout << "Cartesian components (GPa)" << std::endl;
+// if (!std::getline(stream, line) || !std::getline(stream, line) || !std::getline(stream, line)) {
+// std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
+// std::cerr << "Warning: Unexpected end of data when reading stress tensor" << std::endl;
+// }
+// counter++;
+// counter++;
+// counter++;
+// for (size_t i = 0; i < 3; ++i) {
+// if (!std::getline(stream, line)) {
+// std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
+// std::cerr << "Warning: Unexpected end of data when reading stress tensor: " << line << std::endl;
+// break;
+// }
+// counter++;
+// std::istringstream iss(line);
+// std::string tmp;
+// if (!(iss >> tmp >> tmp >> s.stress(i,0) >> s.stress(i,1) >> s.stress(i,2))) {
+// std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
+// std::cerr << "Warning: Unexpected end of data when reading atom forces: " << line << std::endl;
+// }
+// }
+// stress_tensor_bool = true;
+// }
+// // Potential Energy // MD
+// // Total energy corrected for finite basis set = -2690.182502 eV // GO, first step only
+// // enthalpy= indicates end of iteration for GO
+//
+// else if (line.find("Final free energy (E-TS)") != std::string::npos) {
+// if (debug) std::cout << "Final free energy (E-TS)" << std::endl;
+// std::istringstream iss(line);
+// std::string tmp;
+// if (!(iss >> tmp >> tmp >> tmp >> tmp >> tmp >> s.energy)) {
+// std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
+// std::cerr << "Warning: Unexpected end of data when reading total energy" << std::endl;
+// }
+// // scf only loop
+// if (!md_run && !go_run) {
+// s.label = "SCF run: " + std::to_string(scf_idx++);
+// complete_structure = true;
+// }
+// }
+//
+// else if (line.find("enthalpy=") != std::string::npos) {
+// if (debug) std::cout << "enthalpy=" << std::endl;
+// // GO: the last extracted free energy is correct one!
+// std::istringstream iss(line);
+// std::string step;
+// iss >> step >> step >> step >> step; // safe as found enthalpy=
+// std::ostringstream oss;
+// oss << std::boolalpha << constant_volume;
+// s.label = "CASTEP GO, const. volume: " + oss.str() + ", step: " + step;
+// complete_structure = true;
+// }
+//
+// else if (line.find("Potential Energy:") != std::string::npos) {
+// if (debug) std::cout << "Potential Energy:" << std::endl;
+// std::istringstream iss(line);
+// std::string tmp;
+// if (!(iss >> tmp >> tmp >> tmp >> s.energy)) {
+// std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
+// std::cerr << "Warning: Unexpected end of data when reading total energy" << std::endl;
+// }
+// }
+// else if (line.find("Temperature:") != std::string::npos) {
+// if (debug) std::cout << "Temperature:" << std::endl;
+// // MD: end of iteration
+// std::istringstream iss(line);
+// std::string tmp;
+// if (!(iss >> tmp >> tmp >> s.T)) {
+// std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
+// std::cerr << "Warning: Unexpected end of data when reading temperature" << std::endl;
+// }
+//
+// if (!label.size())label = "CASTEP MD, const. volume: false, step: 0"; // the last option
+// s.label = label;
+// complete_structure = true;
+// }
+// if (complete_structure) {
+// if (!stress_tensor_bool) {
+// s.stress.set_zero();
+// }
+// else {
+// s.stress *= p_conv; // GPa -> eV/A^3
+// }
+// stdb.add(s);
+// complete_structure = false;
+// }
+// counter++;
+// }
+//
+// }
+
void CastepCastepReader::print_summary() const {
std::cout << get_summary();
}